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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attattctcatactatggcttaattcagtatcagcatattattaatgttttattaaccatataaataaccaagatttttatctgttacttttttttgcagGTGGTTAATCCATTTACCAA

Basic information

species Glycine max
transcript GLYMA20G32260.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G32260.1 (Glycine max), 3'ss of exon 8
lower sequence: AT3G54830.1 (Arabidopsis thaliana), 3'ss of exon 7
--------------attattctcatactatggcttaattcagtatcagcata----ttattaatgtt--ttattaaccatataaa--taaccaagatttttatctgttacttttttttgcagGTGGTTAATCCATTTACCAA--------------------------------------------
               | |  ||    ||     |||  | |   |  | ||     | | |||  ||  |   || |||  | |    | | |||| |||| |   || | |||||| |||||| |||||||||||||||||                                            
gtaagtttttttttttcacccttcctctgcttattacatgaaagttgggatgattttcactaaatttggtagctagccaggtgaggtcatctaagagtttttttccttgcctttttt-gcagGTTGTTAATCCATTTACCAAATATCCTTTATCAAGAAATATTCAGAGACTTTTCATTTATCTCT
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|209702870|gb|BW655992.1|BW655992
EST:     AACATGCCTAAAGAATTGGTAGCAACCAAGATTGCTGTCTGGACTACG                         GTGGTTAATCCATTTACCAA
genomic: AACATGCCTAAAGAATTGGTAGCAACCAAGATTGCTGTCTGGACTACGgtatacttat ... ttttttgcagGTGGTTAATCCATTTACCAA
EST: gi|16104867|gb|BI892607.1|BI892607
EST:     TTAACATGCCTAAAGAATTGGTAGCAACCAAGATTGCTGTCTGGACTACG                         GTGGTTAATCCATTTACCAA
genomic: TTAACATGCCTAAAGAATTGGTAGCAACCAAGATTGCTGTCTGGACTACGgtatacttat ... ttttttgcagGTGGTTAATCCATTTACCAA
EST: gi|105638003|gb|DY577271.1|DY577271
EST:     AGCAACCAAGATTGCTGTCTGGACTACG                         GTGGTTAATCCATTTACCAA
genomic: AGCAACCAAGATTGCTGTCTGGACTACGgtatacttat ... ttttttgcagGTGGTTAATCCATTTACCAA
EST: gi|9819649|gb|BE555162.1|BE555162
EST:     TTAACATGCCTAAAGAATTGGTAGCAACCAAGATTGCTGTCTGGACTACG                         GTGGTTAATCCATTTACCAA
genomic: TTAACATGCCTAAAGAATTGGTAGCAACCAAGATTGCTGTCTGGACTACGgtatacttat ... ttttttgcagGTGGTTAATCCATTTACCAA
EST: gi|14125144|gb|BG789582.1|BG789582
EST:     TTAACATGCCTAAAGAATTGGTAGCAACCAAGATTGCTGTCTGGACTACG                         GTGGTTAATCCATTTACCAA
genomic: TTAACATGCCTAAAGAATTGGTAGCAACCAAGATTGCTGTCTGGACTACGgtatacttat ... ttttttgcagGTGGTTAATCCATTTACCAA
EST: gi|58017037|gb|CX703779.1|CX703779
EST:     TTAACATGCCTAAAGAATTGGTAGCAACCAAGATTGCTGTCTGGACTACG                         GTGGTTAATCCATTTACCAA
genomic: TTAACATGCCTAAAGAATTGGTAGCAACCAAGATTGCTGTCTGGACTACGgtatacttat ... ttttttgcagGTGGTTAATCCATTTACCAA
EST: gi|193410256|gb|FK377167.1|FK377167
EST:     TTAACATGCCTAAAGAATTGGTAGCAACCAAGATTGCTGTCTGGACTACG                         GTGGTTAATCCATTTACCAA
genomic: TTAACATGCCTAAAGAATTGGTAGCAACCAAGATTGCTGTCTGGACTACGgtatacttat ... ttttttgcagGTGGTTAATCCATTTACCAA
EST: gi|208151014|gb|GD946047.1|GD946047
EST:     TTAACATGCCTAAAGAATTGGTAGCAACCAAGATTGCTGTCTGGACTACG                         GTGGTTAATCCATTTACCAA
genomic: TTAACATGCCTAAAGAATTGGTAGCAACCAAGATTGCTGTCTGGACTACGgtatacttat ... ttttttgcagGTGGTTAATCCATTTACCAA
EST: gi|15202138|gb|BI425242.1|BI425242
EST:     AGCAACCAAGATTGCTGTCTGGACTACG                         GTGGTTAATCCATTTACCAA
genomic: AGCAACCAAGATTGCTGTCTGGACTACGgtatacttat ... ttttttgcagGTGGTTAATCCATTTACCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttttattaaccatataaataaccaagatttttatctgttacttttttttgcagGTGGTTAATCCATTTACCAA
                             tttttatctgttactt  CT-rich tract
             atataaataaccaaga  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attattctcatactatggcttaattcagtatcagcatattattaatgttttattaaccatataaataaccaagatttttatctgttacttttttttgcagGTGGTTAATCCATTTACCAA

- - - ctcatac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaataacc